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Magnesium in PDB 2z75: T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate

Protein crystallography data

The structure of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate, PDB code: 2z75 was solved by D.J.Klein, S.R.Wilkinson, M.D.Been, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.935, 39.942, 70.435, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate (pdb code 2z75). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate, PDB code: 2z75:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 2z75

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Magnesium binding site 1 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:38.4
occ:1.00
 O B:HOH402 2.1 32.5 1.0
O A:HOH401 2.1 31.2 1.0
O B:HOH465 2.1 36.5 1.0
OP2 B:C36 2.2 33.5 1.0
OP2 A:C2 2.3 32.2 1.0
OP2 B:G37 2.3 29.5 1.0
P B:C36 3.3 34.1 1.0
O3' B:A35 3.4 32.0 1.0
P B:G37 3.5 29.6 1.0
P A:C2 3.5 33.1 1.0
O3' A:G1 3.5 31.9 1.0
OP1 B:G37 3.8 30.4 1.0
O2' B:A35 4.1 32.1 1.0
O5' B:C36 4.1 33.3 1.0
C3' B:C36 4.2 29.2 1.0
C5' A:C2 4.2 32.4 1.0
O3' B:C36 4.3 29.4 1.0
O5' A:C2 4.4 32.6 1.0
O2' A:G1 4.5 35.2 1.0
OP1 B:C36 4.5 34.1 1.0
C3' B:A35 4.6 31.1 1.0
OP1 A:C2 4.6 32.2 1.0
C5' B:C36 4.7 31.1 1.0
O5' B:G37 4.7 29.1 1.0
C3' A:G1 4.8 32.3 1.0
C2' B:A35 5.0 30.7 1.0
C8 B:G37 5.0 27.2 1.0
C5' B:G37 5.0 28.2 1.0

Magnesium binding site 2 out of 9 in 2z75

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Magnesium binding site 2 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:42.7
occ:1.00
 C2 B:U79 3.2 57.9 1.0
O2 B:U79 3.2 57.8 1.0
N4 B:C82 3.3 53.1 1.0
O2' B:U79 3.4 56.0 1.0
O B:HOH470 3.5 52.0 1.0
N3 B:U79 3.5 58.5 1.0
C5 B:C81 3.6 51.1 1.0
N4 B:C81 3.6 49.6 1.0
N1 B:U79 3.6 56.8 1.0
C4 B:C81 3.8 51.1 1.0
C2' B:U79 3.9 54.9 1.0
C5 B:C82 3.9 53.4 1.0
C4 B:C82 4.1 53.6 1.0
C1' B:U79 4.2 55.5 1.0
C4 B:U79 4.2 58.8 1.0
C6 B:U79 4.3 57.8 1.0
C6 B:C81 4.4 51.8 1.0
C5 B:U79 4.5 58.6 1.0
N3 B:C81 4.7 51.4 1.0
O4 B:U79 4.9 59.8 1.0

Magnesium binding site 3 out of 9 in 2z75

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Magnesium binding site 3 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:35.6
occ:1.00
 O B:HOH443 2.9 39.0 1.0
O B:HOH457 3.2 36.8 1.0
C4' B:C57 3.2 47.4 1.0
O B:HOH506 3.2 51.3 1.0
O2' B:A56 3.2 40.3 1.0
C5' B:C57 3.2 46.0 1.0
C6 B:U59 3.6 32.7 1.0
O4' B:C57 3.6 47.6 1.0
C2' B:U59 3.9 34.2 1.0
C5 B:U59 3.9 30.9 1.0
C3' B:A58 4.0 38.2 1.0
C5' B:A58 4.0 41.2 1.0
OP1 B:U59 4.0 32.7 1.0
N1 B:U59 4.1 32.2 1.0
C2' B:A56 4.1 39.1 1.0
O5' B:A58 4.2 45.4 1.0
O5' B:U59 4.3 32.9 1.0
O2' B:U59 4.4 34.4 1.0
C4' B:A58 4.5 39.6 1.0
C1' B:U59 4.5 34.0 1.0
O3' B:A58 4.6 35.4 1.0
P B:U59 4.6 33.7 1.0
C3' B:C57 4.6 47.4 1.0
O5' B:C57 4.6 42.3 1.0
C4 B:U59 4.8 32.5 1.0
O3' B:A56 4.9 39.6 1.0
C2 B:U59 4.9 32.5 1.0
C1' B:C57 4.9 47.7 1.0
C2' B:A58 5.0 38.7 1.0
O B:HOH469 5.0 54.4 1.0

Magnesium binding site 4 out of 9 in 2z75

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Magnesium binding site 4 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:57.2
occ:1.00
 O B:HOH544 1.9 52.1 1.0
O B:HOH493 1.9 43.7 1.0
O B:HOH494 2.1 53.3 1.0
O B:HOH492 2.1 43.1 1.0
O B:HOH411 2.2 44.1 1.0
O6 B:G102 3.9 50.0 1.0
O4 B:U100 4.0 57.7 1.0
O6 B:G101 4.1 45.3 1.0
OP2 B:A129 4.2 32.9 1.0
N7 B:G101 4.2 50.3 1.0
OP1 B:A129 4.3 34.7 1.0
N1 B:G102 4.5 47.3 1.0
C6 B:G102 4.5 50.0 1.0
O B:HOH499 4.5 46.1 1.0
C4 B:U100 4.5 57.8 1.0
C5 B:U100 4.6 57.7 1.0
P B:A129 4.8 35.2 1.0
C6 B:G101 4.9 47.6 1.0
C5 B:G101 5.0 48.6 1.0

Magnesium binding site 5 out of 9 in 2z75

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Magnesium binding site 5 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:67.8
occ:1.00
 O B:HOH520 2.5 49.0 1.0
N2 B:G122 3.3 26.4 1.0
O4' B:G123 3.7 29.6 1.0
C1' B:G123 3.7 32.6 1.0
N3 B:G122 3.8 26.2 1.0
C2 B:G122 4.0 28.5 1.0
O2' B:G123 4.4 31.9 1.0
O B:HOH486 4.6 49.0 1.0
C4' B:G123 4.7 31.6 1.0
N9 B:G123 4.7 30.3 1.0
C2' B:G123 4.7 32.4 1.0
O2' B:G122 4.9 30.8 1.0

Magnesium binding site 6 out of 9 in 2z75

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Magnesium binding site 6 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:60.3
occ:1.00
 O B:HOH576 2.2 38.3 1.0
O2P A:GLP201 2.6 53.6 1.0
O A:HOH541 2.6 42.5 1.0
O3P A:GLP201 2.9 56.0 1.0
P A:GLP201 3.2 53.8 1.0
O6 B:G64 3.5 32.5 1.0
C6 A:GLP201 3.6 47.9 1.0
O B:HOH532 3.8 47.0 1.0
N4 B:C63 3.8 40.9 1.0
O6 A:GLP201 4.0 52.2 1.0
N7 B:G64 4.3 37.0 1.0
O6 B:G65 4.4 34.0 1.0
O A:HOH579 4.4 51.5 1.0
C6 B:G64 4.5 33.9 1.0
O1P A:GLP201 4.5 53.7 1.0
C4 B:C63 4.6 42.1 1.0
C5 B:G64 4.8 36.6 1.0
C5 B:C63 4.8 43.5 1.0

Magnesium binding site 7 out of 9 in 2z75

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Magnesium binding site 7 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:67.1
occ:1.00
 O A:HOH577 2.4 44.4 1.0
OP2 B:G61 2.7 41.0 1.0
OP1 B:C60 2.8 36.4 1.0
N6 B:A35 3.7 33.9 1.0
P B:G61 3.7 40.8 1.0
OP1 B:G61 3.8 42.1 1.0
O B:HOH578 3.9 47.2 1.0
O1P A:GLP201 3.9 53.7 1.0
P B:C60 4.0 35.6 1.0
OP2 B:C60 4.3 36.1 1.0
O3' B:C60 4.5 39.8 1.0
O5' B:G61 5.0 39.6 1.0
C6 B:A35 5.0 34.4 1.0

Magnesium binding site 8 out of 9 in 2z75

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Magnesium binding site 8 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg308

b:49.0
occ:1.00
 N7 B:G61 2.8 36.8 1.0
O B:HOH508 2.9 41.6 1.0
O B:HOH425 2.9 33.1 1.0
OP2 B:C60 2.9 36.1 1.0
O6 B:G61 3.0 34.6 1.0
O2' B:G34 3.3 30.8 1.0
C5 B:G61 3.5 36.2 1.0
C6 B:G61 3.6 35.9 1.0
O B:HOH580 3.7 52.2 1.0
C5 B:C60 3.7 33.7 1.0
C8 B:G61 4.0 38.1 1.0
C5' B:U59 4.0 34.0 1.0
O A:HOH579 4.1 51.5 1.0
O B:HOH515 4.2 46.7 1.0
C4 B:C60 4.3 34.2 1.0
N4 B:C60 4.3 32.8 1.0
C6 B:C60 4.4 35.5 1.0
P B:C60 4.4 35.6 1.0
C4' B:U59 4.4 33.8 1.0
C2' B:G34 4.4 31.6 1.0
OP2 B:U59 4.5 32.7 1.0
O A:HOH577 4.6 44.4 1.0
O3' B:G34 4.6 30.5 1.0
N7 B:A35 4.7 33.3 1.0
O5' B:C60 4.8 35.5 1.0
C4 B:G61 4.8 37.0 1.0
O B:HOH578 4.9 47.2 1.0
O6 B:G62 5.0 34.3 1.0
OP2 B:A35 5.0 33.2 1.0
N1 B:G61 5.0 35.2 1.0

Magnesium binding site 9 out of 9 in 2z75

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Magnesium binding site 9 out of 9 in the T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of T. Tengcongensis Glms Ribozyme Bound to Glucosamine-6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg309

b:45.0
occ:1.00
 N7 B:G53 2.7 30.6 1.0
O B:HOH428 2.7 50.1 1.0
O B:HOH581 3.0 47.3 1.0
C8 B:G53 3.5 29.2 1.0
C5 B:C52 3.7 25.6 1.0
C5 B:G53 3.8 28.2 1.0
C4 B:C52 4.0 26.2 1.0
O6 B:G53 4.0 29.9 1.0
O B:HOH488 4.1 47.6 1.0
N4 B:C52 4.1 24.4 1.0
O A:HOH582 4.2 52.8 1.0
C6 B:C52 4.3 24.9 1.0
C6 B:G53 4.3 29.3 1.0
OP2 B:G53 4.4 34.0 1.0
O B:HOH427 4.4 41.0 1.0
N3 B:C52 4.7 27.0 1.0
N9 B:G53 4.8 29.0 1.0
C4 B:G53 4.9 28.9 1.0
OP2 B:C52 5.0 32.4 1.0
N1 B:C52 5.0 29.3 1.0

Reference:

D.J.Klein, S.R.Wilkinson, M.D.Been, A.R.Ferre-D'amare. Requirement of Helix P2.2 and Nucleotide G1 For Positioning the Cleavage Site and Cofactor of the Glms Ribozyme J.Mol.Biol. V. 373 178 2007.
ISSN: ISSN 0022-2836
PubMed: 17804015
DOI: 10.1016/J.JMB.2007.07.062
Page generated: Wed Aug 14 07:47:35 2024

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